When locking the package you can set which file types get included/excluded. The downside is you have to perform this each time and know all the extensions.

What I've been looking into is customizing the Package Types. In 10.0+ there is an XML file you can customize with various Package Type Properties. It's listed under "Package Type-Based Properties" in the Help files. http://www.ptc.com/cs/help/windchill_hc/wc100_hc/index.jspx?id=WCCG_BusLogicCust_WorkPackTypes&action=show
The Type drop down shows up and lets you pick from the types detailed out in the XML file. These types allow you to control Included and excluded types of data.

See also:
https://support.ptc.com/appserver/cs/view/solution.jsp?n=CS101199
Unfortunately I haven't had a chance to fully test it out, but it looks like the functionality you want can be configured through this method. I'm hopeful that it does, because that's the exact same use case we have.